how to distinguish isomer?

hi, everybody

who knows how to distinguish isomer by jchem cartridge api or other methods?

thanks in advance!

 

Hi,

Stereoisomers are distinguished as default. The behaviour is set by the stereo search options:

http://chemaxon.com/jchem/doc/user/query_stereochemistry.html

and

http://chemaxon.com/jchem/doc/user/query_searchoptions.html#optionsSummary

 

Tautomers are distinguished also as default. Their behaviour is ruled by their options:

http://chemaxon.com/jchem/doc/user/query_searchoptions.html#tautomer

 

What kind of isomers do you want to take into account?

Robert

 

rwagner wrote:

Hi, Stereoisomers are distinguished as default. The behaviour is set by the stereo search options: http://chemaxon.com/jchem/doc/user/query_stereochemistry.html and http://chemaxon.com/jchem/doc/user/query_searchoptions.html#optionsSummary   Tautomers are distinguished also as default. Their behaviour is ruled by their options: http://chemaxon.com/jchem/doc/user/query_searchoptions.html#tautomer   What kind of isomers do you want to take into account? Robert

hi, Robert

thanks for your reply, and i have another question, how to generate unique value for compound by structure data, for example, canonical smiles, but when i use api to generate smiles value, it return the same smiles value for isomers.  the following is my code:

   MolImporter importer = new MolImporter(new File("E:\\200909091532.sdf"), "");
   importer.setQueryMode(true);

   MoleculeIterator moleculeIterator = importer.getMoleculeIterator();
   while (moleculeIterator.hasNext()) {
    Molecule molecule = moleculeIterator.next();
    System.out.println(molecule.toFormat("smiles:u"));
   }

   importer.close();

thanks very much!

Attachment contains three isomers.

Hi,

Are you sure that Phosphorus can be chiral in the attached sd file?

As far as I know in this case the componds are not stable enough so the two isomers can interconvert to each other in room temperature.

So that is why we don't interpret the defined wedges, resulting in the same smiles string.

Andras

volfi wrote:

Hi, Are you sure that Phosphorus can be chiral in the attached sd file? As far as I know in this case the componds are not stable enough so the two isomers can interconvert to each other in room temperature. So that is why we don't interpret the defined wedges, resulting in the same smiles string. Andras

hi, Andras

i don't know about it, this data comes from ACD DB.

Thanks.